OK... I think I know why the disappearing books seems so random. I was having the same problem. If I loaded one author everything worked normally, load second author and books were missing, most interesting the content purchased from Amazon always disappeared. In all of my testing, I kept using folders as that did not seem to be related to the issue.

Anyway, I converted both authors to .axw3 format and everything worked as expected. Converted back to .mobi and everything worked as expected. This led me to the conclusion that somewhere in the Calibre past there was a bug that my Kindle Keyboard did not detect that the causes the new Paperwhite software to choke.